Tardigrades, already impossible to kill, also have foreign DNA

Tardigrades, already made of indestructible win, have shown up again in the scientific weirdness Hall of Fame this week, thanks to a new study that sequenced the first tardigrade genome and found that 17.5% of it came from other species. Otherwise known as water bears, tardigrades are actually a large group of related species which have a key trait in common: They’re impossible to kill. Tardigrades are the only species ever observed to survive outside Earth’s sheltering atmosphere. Now scientists are speculating that horizontal gene transfer, the phenomenon identified by a team of researchers at UNC as the reason for the unprecedented proportion of foreign DNA discovered in the tardigrade genome, may also be responsible for some of the tardigrade’s famous durability.

If the idea of fully a sixth of an animal’s genome being of foreign origin seems far-fetched, you’re in good company. Most organisms have a maximum of 1% foreign DNA. Creatures like Elysia chlorotica, which literally consumes a steady diet of other organisms to acquire their powers (of photosynthesis), have been known to science for many years – until now the rotifer, distant cousin to the water bear, was the most extreme example in its class for having acquired about 10% of its DNA from other species via horizontal gene transfer. Even the alarming phenomenon of increasing resistance to antibiotics has its roots in the fact that some single-celled organisms are very good at shaking down other microbes for their spare plasmids. But the proportion of foreign DNA in this clearly successfully adapted organism surprised even the researchers who did the experiment. Bob Goldstein, one of the co-authors of the study, said “We had no idea that an animal genome could be composed of so much foreign DNA. … We knew many animals acquire foreign genes, but we had no idea that it happens to this degree.”

More than a mile beneath the ocean’s surface, as dark clouds of mineral-rich water billow from seafloor hot springs called hydrothermal vents, unseen armies of viruses and bacteria wage war.

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Credit: NOAA

[Click to enlarge image]

More than a mile beneath the ocean’s surface, as dark clouds of mineral-rich water billow from seafloor hot springs called hydrothermal vents, unseen armies of viruses and bacteria wage war.

Like pirates boarding a treasure-laden ship, the viruses infect bacterial cells to get the loot: tiny globules of elemental sulfur stored inside the bacterial cells.

Instead of absconding with their prize, the viruses force the bacteria to burn their valuable sulfur reserves, then use the unleashed energy to replicate.

“Our findings suggest that viruses in the dark oceans indirectly access vast energy sources in the form of elemental sulfur,” said University of Michigan marine microbiologist and oceanographer Gregory Dick, whose team collected DNA from deep-sea microbes in seawater samples from hydrothermal vents in the Western Pacific Ocean and the Gulf of California.

“We suspect that these viruses are essentially hijacking bacterial cells and getting them to consume elemental sulfur so the viruses can propagate themselves,” said Karthik Anantharaman of the University of Michigan, first author of a paper on the findings published this week in the journal Science Express.

Similar microbial interactions have been observed in shallow ocean waters between photosynthetic bacteria and the viruses that prey upon them.

But this is the first time such a relationship has been seen in a chemosynthetic system, one in which the microbes rely solely on inorganic compounds, rather than sunlight, as their energy source.

“Viruses play a cardinal role in biogeochemical processes in ocean shallows,” said David Garrison, a program director in the National Science Foundation’s (NSF) Division of Ocean Sciences, which funded the research. “They may have similar importance in deep-sea thermal vent environments.”

Unusual Bacteria Gobbles Up Carbon in the Ocean

The finding may help researchers better understand how carbon cycling works in marine ecosystems.

“We found that an individual bacterial strain was capable of consuming the same amount of carbon in the ocean as diverse [bacterial] communities,” said study author Byron E. Pedler at the University of California, San Diego.

The researchers found the results surprising because of the immense diversity of molecules that constitute dissolved carbon in one form or another in the ocean, Pedler told Live Science.

Those molecules include both “young” carbon recently produced by phytoplankton — the tiny organisms that are the foundation of the marine food web, and really old carbon that is hundreds of years old. Some of this carbon consists of carbohydrates, but a significant portion of it “is simply uncharacterizable, in that even modern chemical techniques cannot determine what it is,” Pedler said.

Researchers working in the U.S. and Beijing, China report their findings in mBio, the online open-access journal of the American Society for Microbiology.

The routine screening of bees for frequent and rare viruses “resulted in the serendipitous detection of Tobacco Ringspot Virus, or TRSV, and prompted an investigation into whether this plant-infecting virus could also cause systemic infection in the bees,” says Yan Ping Chen from the U.S. Department of Agriculture’s Agricultural Research Service (ARS) laboratory in Beltsville, Maryland, an author on the study.

“The results of our study provide the first evidence that honeybees exposed to virus-contaminated pollen can also be infected and that the infection becomes widespread in their bodies,” says lead author Ji Lian Li, at the Chinese Academy of Agricultural Science in Beijing.

“We already know that honeybees, Apis melllifera, can transmit TRSV when they move from flower to flower, likely spreading the virus from one plant to another,” Chen adds.

Notably, about 5% of known plant viruses are pollen-transmitted and thus potential sources of host-jumping viruses. RNA viruses tend to be particularly dangerous because they lack the 3′-5′ proofreading function which edits out errors in replicated genomes. As a result, viruses such as TRSV generate a flood of variant copies with differing infective properties.

One consequence of such high replication rates are populations of RNA viruses thought to exist as “quasispecies,” clouds of genetically related variants that appear to work together to determine the pathology of their hosts. These sources of genetic diversity, coupled with large population sizes, further facilitate the adaption of RNA viruses to new selective conditions such as those imposed by novel hosts. “Thus, RNA viruses are a likely source of emerging and reemerging infectious diseases,” explain these researchers.

Bee Deaths May Stem From Virus, Study Says

The mysterious mass die-offs of honeybees that have wiped out roughly a third of commercial colonies each year since 2006 may be linked to a rapidly mutating virus that jumped from tobacco plants to soy plants to bees, according to a new study.

The research, reported Tuesday in the online version of the academic journal mBio, found that the increase in honeybee deaths that generally starts in autumn and peaks in winter was correlated with increasing infections by a variant of the tobacco ringspot virus.

The virus is found in pollen that bees pick up while foraging, and it may be spread as the bees mix saliva and nectar with pollen to make “bee bread” for larvae to eat. Mites that feed on the bees may also be involved in transmitting the virus, the researchers said.

Among the study’s authors are leading researchers investigating the bee deaths at the Agriculture Department’s laboratories in Beltsville, Md., as well as experts at American universities and at the Chinese Academy of Agricultural Sciences in Beijing.

Their research offers one explanation for the phenomenon known as colony collapse disorder, in which bees have died at more than twice the usual rate since it was identified seven years ago. But most researchers, including the study’s authors, suspect that a host of viruses, parasites and, perhaps, other factors like pesticides are working in combination to weaken colonies and increase the death rate.

“Huge discoveries remain to be made at the most fundamental level that may change our present conception about the origin of life and its evolution,” says virologist Jean-Michel Claverie, a coauthor of a seminal study, which has been published in this week’s issue of the journal Science.

There are three known domains of life: Bacteria; Archaea, another type of single-celled organism; and Eukaryotes. Scientists believe they may have discovered a fourth domain, a distinct, previously unknown branch of life. A study by the French National Research Agency at Aix-Marseille University that has uncovered two gigantic viruses dubbed “Pandoraviruses” because of the surprises they may hold for biologists -a reference to Pandora, the mythical Greek figure who opened a box and released evil into the world.

Our knowledge of Earth’s microbial biodiversity is still incomplete, says Claverie, who theorizes that the ancient ancestors of Pandoraviruses were once free-living cells that gradually lost most of their genes as they became parasitic. Pandoraviruses may expand our knowledge of life on Earth because they represent a fourth domain of microbial organisms.

One of the viruses, Pandoravirus salinus, was unearthed from sediments collected off the coast of Chile. The other, Pandoravirus dulcis, was discovered in a freshwater pond near Melbourne, Australia. “The fact that two of them were found almost simultaneously from very distant locations either indicate that we were incredibly lucky,” Claverie said, “or that they are not rare.”

In the beginning of their study, the French scientists thought both viruses were the same until they compared the two genome sequences and their encoded proteins, when they realized that the pair represented a new virus family, said Claverie.

To confirm that Pandoraviruses were indeed viruses, the researchers used light and electron microscopes, following their newfound entities through a complete replication cycle. The strange entities met all three key criteria to be labeled viruses.

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